Organizing Your Paper
Review of the Literature
Materials and Methods
References (Literature Cited)
Proofreading and Revising
Common Errors in Research Papers
Additional Things to Avoid

Organizing Your Paper
It might seem simplistic, but before starting to write the paper, take the time to think about and develop a list of points to be made in the paper. As you progress, use lists, outlines, notecards, or whichever strategy works for you to begin to order and to organize those points and ideas into sections.


Review of the Literature
Do an in-depth, balanced review of the primary research literature relevant to your study questions prior to designing and carrying out the experiments. This review will help you learn what is known about the topic you are investigating and may let you avoid unnecessarily repeating work done by others. This literature will form the basis of your Introduction and Discussion. Training in the use of resources such as PubMed and OVID is available from the Reference Librarians.


The function of the Introduction is to establish the context of the work being reported, explain the rationale and background, and to identify the problem you intend to address: in other words, what is the research question, and why is it important to ask it?

  • Begin your Introduction by clearly identifying the subject area of interest. Do this by using key words from your title in the first few sentences of the Introduction to get it focused directly on topic at the appropriate level.
  • Establish the context by providing a brief and balanced review of the pertinent published literature that is available on the subject. The key is to summarize what was known about the specific problem before you did your research.
  • Be sure to clearly state the purpose and /or hypothesis that you investigated. It is most usual to place the statement of purpose near the end of the Introduction, often as the topic sentence of the final paragraph. 
  • Provide a clear statement of the rationale for your approach to the problem studied. State briefly how you approached the problem. Do not discuss here the actual techniques or protocols used in your study, as this will be done in the Materials and Methods section.


Materials and Methods
The Methods section should provide the readers with sufficient detail about the study methods to be able to reproduce the study if so desired. Thus, this section should be specific, concrete, technical, and fairly detailed. The study setting, estimation of sample size, the sampling strategy used, equipment, reagents, cell/tissue samples, data collection methods, and analysis strategies should be described.

  • Describe the context and setting of the study. For example, the study was conducted at a single, tertiary medical center in central Wisconsin.
  • Specify the study design used. Be sure to include the hypotheses you tested, controls, treatments, variables measured, how many replicates you had, what you actually measured, what form the data take, etc.
  • Describe the "population". Did you study patients (human subjects), doctors, hospitals, animals, organisms, genes, etc.?)
  • Describe the sampling strategy. Sampling is simply stated as selecting a portion of the population, in your research area, which will be a representation of the whole population. There are four primary sampling strategies: random sampling, stratified random sampling, systematic sampling, and rational sub-grouping.
  • Describe the intervention (if applicable). This would include any treatment that your study population received.
  • Identify the main study variables. A variable is a concept or abstract idea that can be described in measurable terms. In research, this term refers to the measurable characteristics, qualities, traits, or attributes of a particular individual, object, or situation being studied.
  • Describe data collection instruments and procedures. This would include things such as questionnaires, blood sampling, data queries, etc.
  • Describe how the data were summarized and analyzed. Here you will indicate what types of data summaries and analyses were employed to answer each of the questions or hypotheses tested.

The Methods section is prone to being wordy or overly detailed. Here is some additional advice for writing your Methods section.

  • Avoid repeatedly using a single sentence to relate a single action.
  • Avoid using ambiguous terms to identify controls or treatments, or other study parameters that require specific identifiers to be clearly understood.
  • Be sure to describe the interventions and instruments in sufficient detail.


The purpose of a results section is to present and illustrate your findings. This should be a completely objective report of the results; save all interpretation for the discussion.

  • Report on data collection and recruitment (response rates, etc.) However, do not present the same data more than once.
  • Describe participants. demographic information, clinical condition, etc.
  • Present key findings with respect to the central research question. However, do not discuss or interpret your results, report background information, or attempt to explain anything as this will be covered in Discussion section.
  • Present secondary findings. Secondary outcomes,subgroup analyses, etc.
  • Report negative results - they are important! If you did not get the anticipated results, it may mean your hypothesis was incorrect and needs to be reformulated, or perhaps you have stumbled onto something unexpected that warrants further study. In either case, your results may be of importance to others even though they did not support your hypothesis.
  • Summarize your findings in text and illustrate them, if appropriate, with figures and tables. Note: Text should complement any figures or tables, not repeat the same information.


The purpose of the Discussion is to provide an interpretation of your results and support for all of your conclusions, using evidence from your experiment and generally accepted knowledge, if appropriate. The significance of findings should be clearly described and placed in the context of the topic literature.

  • State the main findings of the study. Decide if each hypothesis is supported, rejected, or if you cannot make a decision with confidence.
  • Discuss the main results with reference to previous research. Explain all of your observations as much as possible. Try to offer alternative explanations if reasonable alternatives exist.
  • Analyse the strengths and limitations of the study. Decide if the experimental design adequately addressed the hypothesis, and whether or not it was properly controlled.
  • Offer perspectives for future work. One study may not answer an overall question, so keeping the big picture in mind, where do you go next? The best studies open up new avenues of research. What questions remain?

The biggest mistakes new writers make in the Discussions is to present a superficial interpretation that simply re-states the results. It is necessary to suggest why the results came out as they did, focusing on the mechanisms behind the observations.


An abstract summarizes, in one or two paragraphs (usually), the major aspects of the entire paper. It might seem backwards, but the Abstract is always the last section written because it is a concise summary of the entire paper. The abstract should include a clear statement of your aims, a brief description of the methods, the key findings, and your interpretation of the key results.

Economy of words is important throughout any paper, but especially in an abstract. Summarize the study, including the following elements in any abstract. Try to keep the first two items to no more than one sentence each.

  • Purpose of the study: hypothesis, overall question, objective.
  • Brief description of the study, including study population/organism.
  • Results, including specific data: If the results are quantitative in nature, report quantitative data; results of any major statistical analysis shoud be reported
  • Important conclusions or questions that follow from the research.
  • Note: As a summary of work done, the abstract is always written in past tense.
  • Note: An abstract should stand on its own, not refer to any other part of the paper (such as a figure or table), and should not include references.

What you report in an abstract must be consistent with what you reported in the paper.


References (Literature Cited)
The Reference section gives a listing of the literature that you actually cited in the body of your paper. Be sure that every citation in your paper is listed in the reference section and vice versa (that every citation in your Reference section is included in the text of your manuscript).

Important Points:

  • Check the journal to which you are submitting your paper for specific instructions on listing and formatting your manuscript. While most medical journals follow AMA style, there are several other styles that may be used. See the Uniform Requirements for Manuscripts Submitted to Biomedical Journals for examples of correct referencing.
  • Do not label this section "Bibliography." A bibliography contains references that you may have read but have not specifically cited in the text.


Proofreading and Revising
Most authors revise their papers at least two to three times. Go back over your paper now and read it carefully; read it aloud. Does it say what you wanted it to say?

  • Check the sequence of ideas/background/content in each section for logical progression.
  • Do any ideas or interpretations need to be moved around within the text to enhance the logical flow of your arguments?
  • Can you shorten long sentences to clarify them?
  • Can you change passive verbs to active forms?
  • Do the Tables and Figures have sufficient information to stand alone outside the context of the paper?
  • Have you checked all your figures and tables? Are the in-text referencing to figures and tables in chronological order?
  • Check for consistent and correct use of terminology.
  • Remove all colloquial language.
  • Check for redundancy (i.e., places where you repeat what you have said elsewhere).
  • Check that all of your sources are cited correctly in the text.


Common Errors in Research Papers

  • The research question is not specified. This may seem simplistic, but not identifying your research question will cause a journal to reject your paper.
  • The structure of the paper is chaotic (e.g., methods are described in the Results section). Stick to the prescribed plan for writing your manuscript and be sure that elements are contained in their proper sections.
  • Verb tense is inconsistent. Use of the wrong verb tense is irritating to read and reflects poorly on the author. When describing methods and results, you should use the past tense. The present tense is appropriate for accepted facts, such as the background information presented in the Introduction. In addition, you may use the present tense when you discuss your results and conclusions.
  • Unnecessary background. If you state facts or describe mechanisms, do so in order to make a point or to help interpret results, and do refer to the present study. Stick to the appropriate point, and include a reference to your source of background information if you feel that it is important.
  • Subjectivity. Subjectivity refers to feelings and opinions. Do not write that you feel or believe something. Present the evidence and suggest strong support for a position, but feelings and beliefs don't come into play.
  • Avoid Superlatives. Superlatives include adjectives such as "huge," "incredible," "wonderful," "exciting," etc. Always use an objective expression, such as "five fold greater."
  • Oversimplification. If a process or procedure is common knowledge in the field, there is no need to detail or explain it.
  • Superficiality. The purpose of a discussion is to interpret the results, not to simply state them in a different way. A superficial discussion ignores mechanisms or fails to explain them completely.
  • Mistakes in reporting data. Properly report converted data rather than raw data. (Raw data include lists of observations, meaurements taken in order to obtain a final result.)
    • Use an appropriate number of decimal places to report means and other measured or calculated values.
    • Ensure that data contained in graphs and tables are accurate and consistent with the text.
    • Do not draw conclusions in the results section. Reserve data interpretation for the discussion.
  • The significance of 'significance'. In science, the word "significant" implies the result of a statistical test. Lack of a statistically significant difference does not mean that the result itself is insignificant. Be prepared to interpret whatever you find, regardless of what you thought you would find.
  • References are out of date or cannot be verfied. Be sure that all your references are cited correctly (i.e., correct authors, journal, year, volume) and your paper cites the most current literature available.
  • The manuscript does not follow the journal's instructions for authors. It is vital that you follow the journal's instructions. You may have a great paper, but failure to follow instructions will cause it to be rejected.
  • The paper is poorly written. Proofread! Incomplete sentences, redundant phrases, obvious misspellings, and other symptoms of a hurriedly-written paper can cost you. Check spelling of scientific names, names of people, names of compounds, etc. Spelling and grammatical errors can be embarrassing. Since many very different terms have similar names, a spelling error can result in a completely incorrect statement. Additionally, be sure to use the correct word, for example affect vs. effect, or assumption vs. deduction.
  • The paper is written in poor English. For non-native writers of English do have a native speaker edit the manuscript.


Additional Things to Avoid

  • Abbreviations: Generally avoid abbreviations. Exceptions include common biological terms like ATP and DNA, units of measure (m, g, cm,) and mathematical or chemical formulas. Sentences should never begin with an abbreviation.
  • Acronyms: Avoid overusing acronyms. The first time an acronym is used it must be spelled out; from that point forward the acronym should be used. An acronym should be used a minimum of three times in a paper. Sentences should never begin with an acronym.
  • Contractions: In formal writing, you should never use contractions.
  • Data: The word "data" is plural, as in "the data were collected."
  • Direct quotes: Direct quotes should be avoided, unless you are presenting another author's specific definition or original label. You can usually paraphrase the writing effectively and more concisely, taking care to properly attribute the sources of your statements.
  • Footnotes: Footnotes should not be used. All citations should be listed in the reference section.
  • Parentheses: Avoid series of parentheses. Do not put a parentheses inside a parentheses.
  • Run-on sentences: Review your writing to make sure that each sentence presents one or two clear ideas. This will also help you organize sentences within paragraphs in a logical order.
  • Scientific names: Names consisting of genus and species, should be underlined or italicized, with only the genus capitalized, for example, Homo sapiens or Ilex opaca.
  • Slang or Colloquial Language: Do not use slang. Try to use precise, scientific terms where possible (without unnecessary jargon) and avoid colloquialisms and figures of speech; for example, use "somewhat" rather than "sort of", or "many" rather than "a lot".
  • Use of However and Therefore: Do not use "however" as a conjunction without a semicolon, (Doxorubicin is a useful chemotherapeutic agent, however severe cardiotoxicity limits its use.) This sentence is a run-on. "However" requires a semicolon or period preceding it, (Doxorubicin is a useful chemotherapeutic agent; however severe cardiotoxicity limits its use) The same holds true for "therefore."
  • Weak pronoun reference: This means the use of it, this, that, these, those, they, and which without clear reference to a noun. Be sure that all pronouns reference a noun.
  • Writing Numbers: In different situations, whether to write a number or use a numeral varies. A fair generality is that a numeral is shorter than a word, so use a numeral, with the following exceptions:
  • Never begin a sentence with a numeral. You will need to spell out the number (eg., one, two million, etc.) If the number involves a unit of measure, the unit must be likewise spelled out as a word in most cases (pH would be one exception). You may want to rework the sentence so you don't have to begin it with the number.
  • When not speaking of data or experimental groupings, use words instead of numerals for numbers less than ten. For example, "two centuries ago", "Five patients were enrolled", "the study was conducted at three centers."
  • Numbers are generally written as numerals when a specific value is named, and always when associated with a unit of measure. For example,"270 centuries ago", "59 people", "47.8 g dry weight".